Warning !! For vertebrate genomes, analyses of complete promoters from co-expressed gene groups return many false positive (i.e. if you submit a random set of genes, you always get plenty of highly 'significant' motifs). This is likely to come from the heterogeneity of human sequences (mixtures of GC-rich and GC-poor promoters).
However, analyses of ChIP-seq peaks return very good results. See the program peak-motifs.